import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.Annotation;
-import jalview.datamodel.DBRefSource;
import jalview.datamodel.SequenceI;
import jalview.io.FileParse;
import jalview.io.StructureFile;
import jalview.schemes.ResidueProperties;
-import jalview.structure.StructureViewSettings;
+import jalview.structure.StructureImportSettings;
import jalview.util.MessageManager;
import java.io.IOException;
@Override
public void parse() throws IOException
{
- String dataName = getDataName();
- if (dataName.endsWith(".cif"))
- {
- setDbRefType(DBRefSource.MMCIF);
- }
- else
- {
- setDbRefType(DBRefSource.PDB);
- }
setChains(new Vector<PDBChain>());
Viewer jmolModel = getJmolData();
jmolModel.openReader(getDataName(), getDataName(), getReader());
if (getId() == null)
{
- setId(inFile.getName());
+ setId(safeName(getDataName()));
}
for (PDBChain chain : getChains())
{
prot.add(chainseq);
}
- if (StructureViewSettings.isPredictSecondaryStructure())
+ if (StructureImportSettings.isProcessSecondaryStructure())
{
createAnnotation(chainseq, chain, ms.at);
}
List<Atom> significantAtoms = new ArrayList<Atom>();
for (org.jmol.modelset.Atom atom : ms.at)
{
+ // System.out.println("Seq Id : " + atom.getSeqID());
+ // System.out.println("To String : " + atom.toString());
+ if (!StructureImportSettings.isProcessHETATMs() && atom.isHetero())
+ {
+ continue;
+ }
if (atom.getAtomName().equalsIgnoreCase("CA")
|| atom.getAtomName().equalsIgnoreCase("P"))
{